Atleltico thumped Real Madrid 5-2 at the Metropolitano, with Carvajal substituted on 59 minutes.
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It has since been confirmed the fullback suffered a calf strain and is now facing an absence of 4-6 weeks.
Carvajal had returned successfully last summer from an ACL injury.
His absence is a blow for Real coach Xabi Alonso, with fellow fullback Trent Alexander-Arnold also sidelined due to injury.